Mac – Can Time Machine backup two HDDs to Time Capsule

Time Machine's thinking is backup everything except what you tell it not to and the time machine hard drive itself. It should not matter how many drives you have connected, they should all be backed up to the time capsule just fine. In other words, you can backup multiple sources but only on one destination, as long as this destination shows up as a single logical drive in the Finder.

Just check in Sys Prefs > Time Machine > Options if the other HD isn't just simply added to the list of exceptions, don't see how it would end up there by itself, but just in case.

And I don't think you can keep working with the same backup, since you divided the data in to 2 separate logical drives. Time Machine just does not think like that. Better start from scratch, perhaps backing up the current backup set to another drive if you need to preserve all the previous backups... Some people need to be able to go back in time to a specific point. I care only to have one up-to-date copy, don't care much about having 30 different ones.

Yes - when you set the Time Machine to back up to the Time Capsule - you will include the internal drive by default. I would let a couple of backups complete, and then go to the settings for time machine under options and make sure the external drive is not excluded. Kick off a a backup with the external drive connected to make sure it works.

If the drive isn't connected when a back up event arrives, the internal will get backed up - but the software will remember and resume backing up the external any time it is connected and a back up happens. You don't need to always have the external drive connected for this to work, you just lose some chances to back it up when it's not connected.